plot_ContUser: Plot user-defined contaminants from evidence.txt

In PTXQC: Quality Report Generation for MaxQuant and mzTab Results

Plot user-defined contaminants from evidence.txt

Description

Kolmogorov-Smirnoff p-values are plotted on top of each group. High p-values indicate that Andromeda scores for contaminant peptides are equal or higher compared to sample peptide scores, i.e. the probability that sample peptides scores are NOT greater than contaminant peptide scores.

Usage

plot_ContUser(data, name_contaminant, extra_limit, subtitle = NULL)

Arguments

data	A data.frame with columns 'fc.raw.file', 'variable', 'value'
name_contaminant	Name of the contaminant shown in title
extra_limit	Position where a h-line is plotted (for visual guidance)
subtitle	Optional subtitle for plot

Value

GGplot object

Examples

 data = data.frame(fc.raw.file = letters[1:3], 
                   variable = c(rep("spectralCount", 3),
                                 rep("intensity", 3),
                                 rep("above.thresh", 3),
                                 rep("score_KS", 3)),
                   value = c(10, 20, 15, 9, 21, 14, 0, 1, 1, 0.3, 0.01, 0.04))
 plot_ContUser(data, "myco", 5, "subtitle")

PTXQC documentation built on July 26, 2023, 5:27 p.m.